paired end reads

Question

[kimaebeloe]

If I have these three files:

SRS052697.denovo_duplicates_marked.trimmed.1.fastq SRS052697.denovo_duplicates_marked.trimmed.2.fastq SRS052697.denovo_duplicates_marked.trimmed.singleton.fastq

does it mean that they are paired end reads?

[John]

SRS052697.denovo_duplicates_marked.trimmed.1.fastq and

SRS052697.denovo_duplicates_marked.trimmed.2.fastq are the files that contain your pairs.

If everything so far has gone right, the first line of .....1.fastq is the first read in the pair, and the first line in the file ......2.fastq is the second read in that pair. You have to provide both files to whatever program you want to read your paired end data.

The singleton file most likely contains reads where one of the two paired reads couldnt be mapped, but the other could. These become "singletons", however, this file is usually useless.

[GouthamAtla]

The singletons are not always useless.

[John]

Usually useless :P

If the pair didn't match, it casts serious doubt on the mapping of the singleton. You can be far more confident of a singleton from single-end-sequencing than from paired-end-sequencing, and it's a mistake to treat them as equals :)

[GouthamAtla]

Yeah. If they became singletons during mapping, they may be less reliable but if at the stage of pre filtering, they are still reliable and useful.

[John]

Yeah, that's a good point :)

Answer 1

[kimaebeloe]

Thanks guys!! Sorry for the late response. I just saw that there were no answers on my post, but now i also learned Answer vs Comments ;)

Kim